Contacts of the strand formed by residues 128 - 134 (chain A) in PDB entry 1BOO
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A PHE* 3.1 8.6 + - - -
127A LEU* 1.3 72.3 - - - +
129A GLU* 1.3 66.3 + - - +
162A TRP* 3.2 44.5 + - + +
164A SER* 3.4 20.4 - - - +
167A GLU 5.9 1.3 - - - -
169A PRO* 4.1 7.0 - - + -
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Residues in contact with GLU 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A LEU* 3.1 8.4 - - - -
128A ALA* 1.3 84.3 - - - +
130A ASP* 1.3 77.5 + - - +
131A PHE* 3.6 12.6 + - + -
162A TRP* 3.3 54.5 + - + +
221A ASN* 3.8 20.0 + - - +
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Residues in contact with ASP 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A LEU* 4.0 21.8 - - + +
129A GLU* 1.3 76.5 - - - +
131A PHE* 1.3 53.0 + - - +
132A TYR* 2.8 34.1 + - - +
160A VAL 4.3 2.9 - - - -
161A TRP* 3.8 17.5 - - + -
221A ASN* 2.4 38.8 + - - +
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Residues in contact with PHE 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A GLU* 3.6 22.9 + - - -
130A ASP* 1.3 75.6 - - - +
132A TYR* 1.3 73.0 + - - +
160A VAL* 2.9 48.1 + - + +
161A TRP* 4.8 0.5 - - - -
162A TRP* 3.8 28.0 - + + +
220A PRO 3.9 20.6 - - - -
221A ASN* 3.4 17.5 - - - -
223A LEU* 3.9 22.2 - - + -
257A PHE* 3.7 32.8 - + - -
258A PHE* 3.8 20.2 - + + -
261A MET* 4.9 7.2 - - + -
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Residues in contact with TYR 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A PHE* 5.9 1.2 - + - -
130A ASP* 2.8 45.9 + - + +
131A PHE* 1.3 81.9 - - - +
133A TRP* 1.3 58.8 + - - +
157A VAL* 4.0 19.3 - - + -
158A ASN 3.5 9.4 - - - -
159A THR* 4.1 21.3 - - + -
160A VAL* 4.8 0.9 - - - -
161A TRP* 3.9 12.4 - + - -
221A ASN* 3.1 24.6 + - + +
222A LEU* 3.4 17.5 - - + +
223A LEU* 3.0 26.5 + - - -
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Residues in contact with TRP 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A ASP* 3.6 32.8 - - - -
132A TYR* 1.3 69.7 - - - +
134A PHE* 1.3 67.2 + - - +
135A ASN* 3.6 24.1 + - + +
156A ALA 3.6 0.9 - - - +
157A VAL* 3.3 6.0 - - - -
158A ASN* 2.9 55.0 + - + +
160A VAL* 3.9 15.6 - - + +
223A LEU* 3.5 19.7 - - + -
225A ILE* 3.0 35.6 + - + +
227A ASN* 5.1 1.6 - - + -
249A ARG 5.3 1.3 - - - -
250A PHE* 3.8 8.1 - - + -
251A PRO* 3.3 38.8 - - + -
254A LEU* 3.8 22.2 - - + -
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Residues in contact with PHE 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A TYR 3.9 1.6 + - - -
133A TRP* 1.3 70.7 - - - +
135A ASN* 1.3 57.5 + - - +
136A PRO* 3.2 31.5 - - + +
156A ALA* 3.4 33.7 - - + -
157A VAL* 4.0 13.0 - - + -
222A LEU* 4.0 20.2 - - + -
223A LEU 2.9 12.9 + - - +
224A GLN* 3.4 44.0 - - + -
225A ILE 2.9 22.5 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il